RetrogeneDB ID: retro_pabe_576

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:25655485..25655899(-)
• Located in intron of: ENSPPYG00000002156

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: COQ10B
• Ensembl ID: ENSPPYG00000013045
• Aliases: None
• Description: Coenzyme Q-binding protein COQ10 homolog B, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q5RD79]

Sequence

>retro_pabe_576
AGTGGTCGGAGCCCTGGCTCAGAGGGGCCTGAGCAGAACATCCGATATTTAGCTTCCTGTGGTATACTGATGAGCAGAGC
TCTTCCGCTACATATGTCATTTTTGATTAAGGAGATATGTGCAATAACTTTCTTCACAATCGCTGCACCATTAATAAACA
AAAGGAAATATTCAGAGAGGAGGATTTTAGGCTATTTAATGCAGGAAATGTATGATGTTGTATTGGGAATGGAGGATTAT
AAGCATTTCATTCTTTGGTGCAAAAAATCAGATATAATATCAGAGAGATCTGGATATTACAAAACACAATTAGAAATTGA
GTTTCCAGCAGTGTTGGAGTGATATTCAGCAGTGACCTTGGTGAAACCTCATTTGGTAAAGGTATCCTGTACTGATGGGA
GACTTTTCAAGCAT

Alignment

ORF - retro_pabe_576 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.71 %
• Parental protein coverage: 58.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SATAAGAQAPVRNGRYLASCGILMSRTLPLHTSILPKEICARTFFKITAPLINKRKEYSERRILGYSMQE
          S....G...P..N.RYLASCGILMSR.LPLH.S.L.KEICA.TFF.I.APLINKRK.YSERRILGY.MQE
Retrocopy SGRSPGSEGPEQNIRYLASCGILMSRALPLHMSFLIKEICAITFFTIAAPLINKRK-YSERRILGYLMQE

Parental  MYDVVSGVEDYKHFVPWCKKSDVISKRSGYCKTRLEIGFPPVLERYTSVVTLVKPHLVKASCTDGRLFNH
          MYDVV.G.EDYKHF..WCKKSD.IS.RSGY.KT.LEI.FP.VLE.Y.S.VTLVKPHLVK.SCTDGRLF.H
Retrocopy MYDVVLGMEDYKHFILWCKKSDIISERSGYYKTQLEIEFPAVLE*Y-SAVTLVKPHLVKVSCTDGRLFKH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.06 RPM	15.09 RPM
SRP007412_cerebellum	0.00 RPM	10.34 RPM
SRP007412_heart	0.00 RPM	14.75 RPM
SRP007412_kidney	0.00 RPM	15.31 RPM
SRP007412_liver	0.00 RPM	11.05 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_576 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_576 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_576 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_569
Macaca mulatta	retro_mmul_2434

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004659	2 retrocopies	retro_btau_1595, retro_btau_1832,
Choloepus hoffmanni	ENSCHOG00000005807	1 retrocopy	retro_chof_1504,
Callithrix jacchus	ENSCJAG00000003971	1 retrocopy	retro_cjac_1836,
Dasypus novemcinctus	ENSDNOG00000003229	2 retrocopies	retro_dnov_1571, retro_dnov_2203,
Dipodomys ordii	ENSDORG00000004090	1 retrocopy	retro_dord_508,
Erinaceus europaeus	ENSEEUG00000001626	1 retrocopy	retro_eeur_401,
Felis catus	ENSFCAG00000022385	1 retrocopy	retro_fcat_1487,
Homo sapiens	ENSG00000115520	1 retrocopy	retro_hsap_3349,
Gorilla gorilla	ENSGGOG00000023373	2 retrocopies	retro_ggor_2270, retro_ggor_569,
Myotis lucifugus	ENSMLUG00000000865	1 retrocopy	retro_mluc_1236,
Macaca mulatta	ENSMMUG00000010488	1 retrocopy	retro_mmul_2434,
Monodelphis domestica	ENSMODG00000012281	1 retrocopy	retro_mdom_600,
Mus musculus	ENSMUSG00000025981	1 retrocopy	retro_mmus_3224,
Nomascus leucogenys	ENSNLEG00000006871	1 retrocopy	retro_nleu_1172,
Ochotona princeps	ENSOPRG00000010091	3 retrocopies	retro_opri_1020, retro_opri_173, retro_opri_664,
Pongo abelii	ENSPPYG00000013045	2 retrocopies	retro_pabe_2758, retro_pabe_576 ,
Pan troglodytes	ENSPTRG00000012772	1 retrocopy	retro_ptro_2137,
Rattus norvegicus	ENSRNOG00000014456	1 retrocopy	retro_rnor_1620,
Tarsius syrichta	ENSTSYG00000012642	2 retrocopies	retro_tsyr_1213, retro_tsyr_1666,